Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy

Weisong Zhao; Shiqun Zhao; Liuju Li; Xiaoshuai Huang; Shijia Xing; Yulin Zhang; Guohua Qiu; Zhenqian Han; Yingxu Shang; De-En Sun; Chunyan Shan; Runlong Wu; Lusheng Gu; Shuwen Zhang; Riwang Chen; Jian Xiao; Yanquan Mo; Jianyong Wang; Wei Ji; Xing Chen; Baoquan Ding; Yanmei Liu; Heng Mao; Bao-Liang Song; Jiubin Tan; Jian Liu; Haoyu Li; Liangyi Chen

doi:10.1038/s41587-021-01092-2

Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy

Nat Biotechnol. 2022 Apr;40(4):606-617. doi: 10.1038/s41587-021-01092-2. Epub 2021 Nov 15.

Authors

Weisong Zhao^#¹, Shiqun Zhao^#², Liuju Li^#², Xiaoshuai Huang³, Shijia Xing², Yulin Zhang², Guohua Qiu¹, Zhenqian Han¹, Yingxu Shang⁴, De-En Sun⁵, Chunyan Shan⁶, Runlong Wu², Lusheng Gu⁷, Shuwen Zhang⁷, Riwang Chen⁸, Jian Xiao⁹, Yanquan Mo², Jianyong Wang⁸, Wei Ji⁷, Xing Chen⁵, Baoquan Ding⁴, Yanmei Liu^{2

10}, Heng Mao¹¹, Bao-Liang Song⁹, Jiubin Tan^{12

13}, Jian Liu^{1

14}, Haoyu Li^{15

16

17}, Liangyi Chen^{18

19

20}

Affiliations

¹ Advanced Microscopy and Instrumentation Research Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China.
² State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China.
³ Biomedical Engineering Department, Peking University, Beijing, China.
⁴ CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China.
⁵ College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
⁶ College of Life Sciences, Peking University, Beijing, China.
⁷ National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
⁸ School of Software and Microelectronics, Peking University, Beijing, China.
⁹ Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China.
¹⁰ Institute for Brain Research and Rehabilitation (IBRR), Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China.
¹¹ School of Mathematical Sciences, Peking University, Beijing, China.
¹² Center of Ultra-Precision Optoelectronic Instrument Engineering, Harbin Institute of Technology, Harbin, China.
¹³ Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China.
¹⁴ Key Laboratory of Micro-Systems and Micro-Structures Manufacturing of Ministry of Education, Harbin Institute of Technology, Harbin, China.
¹⁵ Advanced Microscopy and Instrumentation Research Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China. lihaoyu@hit.edu.cn.
¹⁶ Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China. lihaoyu@hit.edu.cn.
¹⁷ Laboratory for Space Environment and Physical Sciences, Harbin Institute of Technology, Harbin, China. lihaoyu@hit.edu.cn.
¹⁸ State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China. lychen@pku.edu.cn.
¹⁹ PKU-IDG/McGovern Institute for Brain Research, Beijing, China. lychen@pku.edu.cn.
²⁰ Beijing Academy of Artificial Intelligence, Beijing, China. lychen@pku.edu.cn.

^# Contributed equally.

PMID: 34782739
DOI: 10.1038/s41587-021-01092-2

Abstract

A main determinant of the spatial resolution of live-cell super-resolution (SR) microscopes is the maximum photon flux that can be collected. To further increase the effective resolution for a given photon flux, we take advantage of a priori knowledge about the sparsity and continuity of biological structures to develop a deconvolution algorithm that increases the resolution of SR microscopes nearly twofold. Our method, sparse structured illumination microscopy (Sparse-SIM), achieves ~60-nm resolution at a frame rate of up to 564 Hz, allowing it to resolve intricate structures, including small vesicular fusion pores, ring-shaped nuclear pores formed by nucleoporins and relative movements of inner and outer mitochondrial membranes in live cells. Sparse deconvolution can also be used to increase the three-dimensional resolution of spinning-disc confocal-based SIM, even at low signal-to-noise ratios, which allows four-color, three-dimensional live-cell SR imaging at ~90-nm resolution. Overall, sparse deconvolution will be useful to increase the spatiotemporal resolution of live-cell fluorescence microscopy.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Imaging, Three-Dimensional* / methods
Microscopy, Fluorescence / methods